Weekly coronavirus-related chat, questions, and minor updates - week of November 16

More evidence that Covid Winter will be extraordinarily bad: The National Respiratory and Enteric Virus Surveillance System (NREVSS) National Trends shows the past two years' history of four non-COVID-19 coronaviruses. These start to appear in testing around mid-October, peak from late December to April, and fade by late-May to June.

This suggests that the January-April emergence of COVID-19 actually occurred about halfway through the peak season, attenuating spread compared to a full-length outbreak.

More evidence comes when looking at South American and African data. For much of the period June through September, South America performed conspicuously poorly for COVID spread. This increasingly looks like a wintertime peak.

Africa as a whole has been relatively spared, and hasn't shown a strong seasonal trend. But Africa also spans both Northern and Southern hemispheres. Southern Africa generally, and the country that has seen the largest outbreak, South Africa, also seems to show a winter peak. Cases are now trending high in Morocco, in North Africa.

The other southern region, Oceania, has fared well, though again Australia’s peak spans winter.

European cases began rising notably in September. A friend teaching at university in the UK has been posting regular updats and as of early October was showing cases doubling every two days --- relatively low numbers, but it's the growth rate that matters. More broadly, cases started rising noticeably September--October. This was about 4--8 weeks ahead of the US rise, and in both cases more northerly regions seem first affected.

If this is accurate, then we may well be on the cusp of an extraordinarily bad Covid Winter, with infection peaks occurring in February--March.

Interventions, including lockdowns, masks, and vaccines (available likely March--June) should help, but this looks like it's going to be quite bad, with peak infection and death rates 4-8 times levels being seen possible.

The good news is that European case growth has slowed, flattened, or declined in many countries, for now. Quarantine does in fact work. But there's six months between now and June.

On Sunday Michigan governor Gretchen Whitmer announced closures and restrictions affecting resteraunts, movie theaters, colleges and highschools starting in Wednesday.

Mike Duggan, the mayor is Detroit, places blame on the suburbs around Detroit not behaving themselves.

I've been waiting for this for weeks. Michigan's average cases per day is now over 6000, almost 10x higher than it was in March when our first shutdown occurred. Meanwhile our Republican legislature has done shit all to offer any relief or comprehensive plan, aside from play legal games in court with Whitmer over her executive authority to declare a State of Emergency. So now instead of using her executive authority, instead the department off health just issues the same restrictions.

Usual personal update:

I'm tired. Exhausted. There's not a lot of gas left in my tank. Healthcare workers, my heart goes out to you. I know only a tiny fraction of your fatigue, and it's devastating.

Today the outlet running one of my HEPA filters shorted out. I didn't realize it at the time and felt a potent horror fall over me as I looked down and saw that the filter unit was completely off. My kids laughed at the physical comedy of me frantically trying to figure out what went wrong and how to get it running again. I'll admit that I probably looked funny from the outside because I wasn't paying attention at all to how I was coming across and was instead panicking in sheer terror to get it back up and running. There's unfortunately nothing funny about that at all.

A couple of days ago a substitute teacher had closed all the windows in a room because it was cold. We rotate rooms between periods, so when I entered the room, the students had been in an unventilated space (with no filters running) for the better part of an hour. I have given them numerous speeches about how important it is to have the windows open (and how they need to make sure they're open for their own safety even if we teachers or even any adults aren't present), but those sermons don't get heard when they're literally shivering in their seats. The immediate comfort of warmth overrides the invisible and unclear threat of COVID. And we're not even close to real winter yet.

I also said last week, in a retraction from a previous week, that I didn't see any way for us to shut down because they're not counting anyone as close contacts on account of distancing. I'm here with yet again another retraction; this time a re-retraction. I'm back to believing that we will shut down, but it won't be because of confirmed COVID cases -- it'll be because too many teachers are self-quarantining due to suspected exposures and they won't have enough substitutes to run the building.

This seems like the appropriate response to a bunch of people protesting against restrictions literally designed to save their lives and the lives of people near them. I wish the US would treat it as seriously. Berlin Police Disperse Anti-Lockdown Protesters With Water Cannons

The most clear outlier here concerning Covid cases is class and economic status. Basically - if you don't have any margins, or if you have a larger family living in a smaller space, or if you work somewhere where even sickpay isn't going to cut it - any for of self-quarantine wont matter.

Since a hard lockdown isn't legally possible (unless they declare war on something there is no legal framework for it) the sickness spread fastest in larger cities where those of lower classes or with lower economic status live in the suburbs as public transport is critical to them.

EDIT: still fascinated by moralism as a driving force in the western left in many countries in the way they react to the Covid threat and why thats scary AF.

More than 2,500 nurses at four Philadelphia area hospitals are preparing to go on strike in the coming days.

Nearly a quarter of American hospitals are running out of workers

New York City is stopping in-person classes at all of their public schools again as of tomorrow, basically meaning teachers only have overnight to figure that out. The NYT's reporter for NY schools is pretty impressed by the whole thing.

The US has also crossed a total of 250,000 deaths now.

Amid COVID-19 travel warnings, California lawmakers fly to Hawaii

More than half a dozen California lawmakers are among the 50 people attending a policy conference sponsored by the Independent Voter Project, a nonprofit group, at the Fairmont Kea Lani Hotel in Wailea, with some legislators’ travel expenses picked up by the hosts. The four-day conference, at which panel participants discuss various issues including how to reopen states safely amid COVID-19, began Monday.

Even under non-pandemic circumstances, this seems like a sketchy pseudo-vacation and of questionable ethics (though it probably complies with the letter of the ethical rules if not their spirit). It's the week before Thanksgiving so not a whole lot is getting done, perfect time to escape to Maui for a conference.

Sure enough:

The annual gathering, which has seen up to 25 California lawmakers in attendance in past years, has faced criticism because it is partly financed and attended by special interests, including businesses and labor groups, that lobby legislators.

Mysteries of COVID Smell Loss Finally Yield Some Answers

Olfactory neurons do not have angiotensin-converting enzyme 2 (ACE2) receptors, which allow the virus entry to cells, on their surface. But sustentacular cells, which support olfactory neurons in important ways, are studded with the receptors. These cells maintain the delicate balance of salt ions in the mucus that neurons depend on to send signals to the brain. If that balance is disrupted, it could lead to a shutdown of neuronal signaling—and therefore of smell.

The sustentacular cells also provide the metabolic and physical support needed to sustain the fingerlike cilia on the olfactory neurons where receptors that detect odors are concentrated. “If you physically disrupt those cilia, you lose the ability to smell,” Datta says.

In a study in Brain, Behavior and Immunity, Nicolas Meunier, a neuroscientist at the Paris-Saclay University in France, infected the noses of golden Syrian hamsters with SARS-CoV-2. Just two days later, about half of the hamsters’ sustentacular cells were infected. But olfactory neurons were not infected even after two weeks. And strikingly, the olfactory epithelia were completely detached, which, Meunier says, resembled skin peeling after a sunburn. Although olfactory neurons were not infected, their cilia were entirely gone. “If you remove the cilia, you remove the olfactory receptors and the ability to detect odorants,” he says.

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More clues to how the virus obliterates smell come from people recovering from anosmia. “The majority of patients lose smell like a light switch going off and recover it rapidly,” Datta says. “There’s a fraction of patients that have much more persistent anosmia and recover on longer time scales.” The olfactory epithelium regularly regenerates. “That’s the body’s way of protecting against the constant onslaught of toxins in the environment,” Meunier says.

‘People are going to die’: Hospitals in half the states are facing a massive staffing shortage as Covid-19 surges

Staffing shortages are a serious concern in multiple regions. Intensive care unit nurses, who typically oversee no more than two patients at a time, are now being pushed to care for six to eight patients to make up for the shortfall in parts of Texas, said Robert Hancock, president of the Texas College of Emergency Physicians. In Ohio, some 20% of the 240 hospitals tied to the Ohio Hospital Association are reporting staffing shortages, according to spokesperson John Palmer.

The American Hospital Association’s vice president of quality and patient safety, Nancy Foster, said she’s heard from two dozen hospital leaders over the past two weeks, warning her of staffing shortages in states including Texas, North and South Dakota, Minnesota, Wisconsin, and Illinois. Health care providers in Kansas, Oklahoma, Arkansas, Ohio, Missouri, Michigan, and Utah said they’re facing the same problem, as do local reports from New Mexico, Nebraska, Colorado, Wyoming, Tennessee, Georgia, Alabama, Indiana, Montana, California, Rhode Island, and South Carolina.

If you're curious about one of those states, there are links in the article. For California, it links to:

UCLA, UC Irvine nurses rally over COVID exposure, staff shortages

Back to the first article:

The situation is exacerbated as staff get sick with coronavirus themselves, or else have to quarantine after exposure. The staffing need is so dire, hospital workers who have tested positive for Covid-19 but are asymptomatic have been told to continue working in North Dakota.

One rural hospital in Texas is struggling with 30% of staff nurses out of commission because of infection with or exposure to Covid-19, said TORCH’s Henderson. At one point earlier this month, more than 1,000 staff from the Mayo Clinic were out of work because of Covid-19, said Amy Williams, executive dean of Mayo Clinic Practice.

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As health care systems compete for additional staff, salaries skyrocket. ICU nurses are a “hot commodity,” said Dan Weberg, a former emergency room nurse and head of clinical innovation at Trusted Health, and their fees are currently twice as much as pre-Covid rates, at around $5,000 to $6,000 per week.

Idaho public health board invites anti-mask conspiracy theorists to talk COVID-19

Idaho is “a victim of a very sophisticated psy-ops, psychological warfare,” said Dr. Vicki Wooll, who shared conspiracy theories during her presentation. “It’s getting us through social media. We are not the enemy. The enemy is coming from without.”

Among other things, Wooll claimed that 5G wireless internet may be tied to COVID-19 — a false theory that was spread on social media.

The Coronavirus Is Airborne Indoors. But We’re Still Scrubbing Surfaces.

Hand washing with soap and water for 20 seconds — or sanitizer in the absence of soap — is still encouraged to stop the virus’s spread. But scrubbing surfaces does little to mitigate the virus threat indoors, experts say, and health officials are being urged to focus instead on improving ventilation and filtration of indoor air.

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Early on, officials required Hong Kong restaurants to install dividers between tables — the same sort of flimsy, and essentially useless, protection used at the U.S. vice-presidential debate in October.

But as the Hong Kong authorities have gradually eased restrictions on indoor gatherings, including allowing wedding parties of up to 50 people, there is a fear of potentially new outbreaks indoors.

Some experts say they are especially concerned that coronavirus droplets could spread through air vents in offices, which are crowded because the city has not yet developed a robust culture of remote work.

“People are removing masks for lunch or when they get back to their cubicle because they assume their cubicle is their private space,” said Yeung King-lun, a professor of chemical and biological engineering at the Hong Kong University of Science and Technology.

“But remember: The air you’re breathing in is basically communal.”

7 dead, nearly 200 test positive for COVID-19 following Maine wedding

An Ohio wedding had 83 guests. More than a third, including the newlyweds, got the coronavirus.

Washington state wedding with 300 guests turns into a COVID-19 super-spreader event

Italy is again seeing one of the world’s highest coronavirus death tolls, but it no longer registers as a national tragedy

Coronaviruses closely related to the pandemic virus discovered in Japan and Cambodia

Two lab freezers in Asia have yielded surprising discoveries. Researchers have told Nature they have found a coronavirus that is closely related to SARS-CoV-2, the virus responsible for the pandemic, in horseshoe bats stored in a freezer in Cambodia. Meanwhile, a team in Japan has reported the discovery of another closely related coronavirus — also found in frozen bat droppings.

The viruses are the first known relatives of SARS-CoV-2 to be found outside China, which supports the World Health Organization’s search across Asia for the pandemic’s animal origin. Strong evidence suggests that SARS-CoV-2 originated in horseshoe bats, but whether it passed directly from bats to people, or through an intermediate host, remains a mystery.

The virus in Cambodia was found in two Shamel’s horseshoe bats (Rhinolophus shameli) captured in the country’s north in 2010. The virus’s genome has not yet been fully sequenced — nor its discovery published — making its full significance to the pandemic hard to ascertain.

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Duong’s team captured the Shamel’s horseshoe bats in Cambodia as part of the US-government-funded PREDICT project, which surveyed wildlife worldwide for viruses with pandemic potential for decades and ended earlier this year. In April, the US Agency for International Development gave the programme an additional US$3 million and a 6-month extension to look for evidence of SARS-CoV-2 in animal samples — mostly bats, as well as pangolins and other animals — that were sitting in laboratory freezers in Laos, Malaysia, Nepal, Thailand, Vietnam, and Cambodia. A full report of these investigations is expected in the coming weeks.